Contacts of the strand formed by residues 60 - 67 (chain B) in PDB entry 1KTZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 60 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 4.3 5.8 - - - -
28B CYS* 3.8 5.4 - - - -
58B GLN 3.9 8.3 - - - +
59B GLU* 1.3 79.1 - - - +
61B CYS* 1.3 70.6 + - - +
78B CYS* 3.3 4.7 - - - -
79B HIS 2.9 42.0 + - - +
81B PRO* 4.1 14.4 - - + -
90B LEU* 4.2 7.4 - - + -
93B ALA* 4.1 23.8 - - + +
114B SER* 4.1 9.4 - - - -
115B CYS 3.4 11.4 - - - +
116B SER* 3.9 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 3.3 19.5 - - - -
27B LEU 3.3 5.4 - - - -
28B CYS* 2.0 48.2 - - - -
60B VAL* 1.3 72.2 - - - +
62B VAL* 1.3 60.8 + - - +
77B VAL 3.7 2.0 - - - -
114B SER* 3.0 9.5 - - - -
115B CYS* 2.9 35.7 + - - +
117B SER 4.1 0.4 - - - -
120B CYS* 3.6 20.9 - - - -
121B ASN* 3.6 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.3 2.7 - - + +
61B CYS* 1.3 81.6 - - - +
63B ALA* 1.3 67.7 + - - +
64B VAL* 4.1 12.3 - - + -
75B GLU 4.4 0.4 - - - +
76B THR* 3.4 0.9 - - - -
77B VAL* 2.9 31.5 + - + +
79B HIS* 3.7 20.0 - - + -
85B TYR* 4.1 24.7 - - + -
90B LEU* 3.6 31.2 - - + -
112B MET* 4.3 7.6 - - + -
113B CYS 3.5 9.0 - - - +
114B SER* 4.3 1.6 - - - -
121B ASN* 2.9 20.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 1.3 76.3 - - - +
64B VAL* 1.3 63.8 + - - +
74B LEU* 4.4 5.4 - - + -
75B GLU 3.1 7.9 - - - +
76B THR* 4.4 2.2 - - + -
98B CYS* 3.9 3.6 - - - -
100B MET* 3.7 4.9 - - + +
112B MET* 3.4 5.9 - - - +
113B CYS* 3.0 40.3 + - - +
121B ASN* 4.1 9.6 - - + +
124B ILE* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 4.1 9.2 - - + -
63B ALA* 1.3 79.6 - - - +
65B TRP* 1.3 62.3 + - - +
66B ARG* 3.8 17.1 + - - +
73B THR 3.7 1.2 - - - +
74B LEU* 3.2 7.1 - - - +
75B GLU* 2.7 63.0 + - + +
85B TYR* 4.4 1.6 - - + -
86B HIS* 3.9 9.4 - - + -
110B PHE* 3.5 33.0 - - + -
111B PHE 3.4 7.2 - - - +
112B MET* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 5.0 1.6 - - - -
38B CYS* 2.8 51.0 + - + -
39B ASP* 3.8 17.0 - - - -
40B ASN 5.7 0.2 - - - -
64B VAL* 1.3 74.8 - - - +
66B ARG* 1.3 64.9 + - - +
67B LYS* 3.6 28.5 - - + -
72B ILE* 3.4 24.1 - - + +
73B THR 3.4 6.5 - - - -
74B LEU* 4.3 5.8 - - + -
100B MET* 3.8 19.4 - - + +
109B THR* 3.8 27.6 - - + -
110B PHE* 3.5 0.2 - - - -
111B PHE* 2.8 57.0 + + + +
124B ILE* 4.5 4.5 - - + -
126B PHE* 3.8 16.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 6.3 1.3 - - - -
64B VAL* 3.8 23.3 - - + +
65B TRP* 1.3 77.4 - - - +
67B LYS* 1.3 60.6 + - - +
68B ASN 4.3 0.4 - - - -
71B ASN* 3.9 1.0 - - - +
72B ILE* 3.3 3.9 - - - +
73B THR* 2.8 58.7 + - - +
75B GLU* 5.2 2.8 + - - -
86B HIS* 3.5 29.3 + - - -
105B LYS* 3.6 17.8 - - - +
108B GLU* 2.7 48.6 + - - +
109B THR 3.2 6.1 - - - +
110B PHE* 3.5 12.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASP* 2.8 33.5 + - - +
40B ASN* 5.1 4.0 - - - +
65B TRP* 3.6 28.9 - - + -
66B ARG* 1.3 76.6 - - - +
68B ASN* 1.3 70.1 + - - +
71B ASN 3.4 4.3 - - - +
72B ILE* 3.8 19.3 - - + -
108B GLU* 3.3 4.7 - - - -
109B THR* 2.9 42.3 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il